Level III Registration to NIF

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Level III Registration to NIF Case Study - SumsDB
David C. Van Essen
Building an Information Framework for
Neuroscience Natcher Center, NIH 19 October, 2007
Washington University in St. Louis
Supported by the Human Brain Project (NIMH, NSF,
NCI, NLM, NASA)
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SumsDB (Surface Management System Database)
http//sumsdb.wustl.edu/sums/
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SumsDB Database Attributes

• Diverse in many respects
• Many species (human, macaque, rodents, apes)
• Surfaces (cerebral, cerebellar cortex) and
  volumes
• Atlases individuals
• Different ages, disease conditions
• Diverse data overlays (gt 50 data types)
• Functional MRI activations
• Stereotaxic coordinates (foci)
• Surface morphometry
• Connectivity
• Published, unpublished datasets
• Data access online visualization (WebCaret)
  download
• Search options coordinates regional labels
  functional attributes

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SumsDB

• Current status
• 42 Gb archived data
• 12 Gb public data
• 70,000 files (archives)
• Since 2005
• 14,000 archive downloads for offline analyses
• 10,000 WebCaret launches
• 30 active user accounts (data upload)

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SumsDB - Level III Registration

• How to get started?
• Focus on (stereotaxic) foci (a well-defined,
  well-characterized dataset)
• Current status
• 13,000 published stereotaxic coordinates
• 450 studies
• Rich but concise dataset, excellent for data
  mining

13,00 foci displayed using Caret
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SumsDB - Level III Registration
Extensive metadata associated with each focus
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Add Foci Attributes
Select multiple partitioning schemes
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Add Foci Attributes
Cortical area assignments (multiple partitioning
schemes) Allows search by area (as well as
spatial coordinates)
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Level III Registration to NIF Mediator

• Requirements
• Create and register export schema
• (subset of primary schema)
• Map relevant terminology
• Start with Brodmann areas
• Create SumsDB user account (nifsums on
  BIRNportal)
• (read-only access to portion of SumsDB)
• Done by
• Local DB admin (Ping Gu)
• NIF developers (Vadim Astakhov et al.)

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SumsDB primary schema (70 tables)
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Tables specific for stereotaxic foci
three other tables
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Create birnsums schema view for public foci
data
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Level III Registration to NIF Mediator

• Technical issues
• Firewall issues (resolved by departmental
  sys-admin)
• Start with SumsDB development site (minimize
  risks)
• Restrict access to foci-related data.

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Mapping to Level 3 A practical experience

• Mapping data values from SumsDB to NIFSTD
• Brodmann.10 etc. database-specific shorthand
  
• Concept Term Mapper Provides access to NIFSTD
  vocabulary

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Why is this currently done by a human?

• Abbreviations, ambiguous terms, non-standard
  names, e.g.,
• LPF (if this is mapped as an abbreviation to
  NIFSTD, then it wouldnt be a problem)
• Anterior cingulate Gyrus? Sulcus?
• Frontal subgyral frontal subgyral white matter?

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Results! Search NIF for dopamine, view SumsDB
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Search NIF for dopamine, view CCDB
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Search NIF for dopamine, view NeuroMorpho
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Results! Search NIF for cerebellum, view SumsDB
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Search NIF for cerebellum, view CCDB
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Search NIF for cerebellum, view Senselab
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Search NIF for Brodmann area 19, view SumsDB
OK, but what if I want to view these foci on the
atlas?
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Currently, must launch SumsDB, search for
Brodmann.19
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View search results in SumsDB
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Display search results in WebCaret
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Possible Next Steps

• Expand search vocabulary
• multiple partitioning schemes cortical sulci
  gyri
• Establish process for updating NIF foci-related
  cache
• Export NIF search results, display on WebCaret
• Incorporate other data types (fMRI maps)
• Extend to macaque, mouse, rat datasets
• Establish level 3 links with additional
  databases, e.g.
• Brainmap (stereotaxic foci P. Fox)
• BrainInfo (macaque D. Bowden)
• Allen Brain Atlas (mouse gene expression)
• fMRIDC (human M. Gazzaniga)
• Brainmaps.org (histology E.G. Jones)
• CoCoMac (connectivity R. Kotter)

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Example 1. fMRI data in different databases
Search area (SumsDB), high expression (ABA)
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Example 2. Gene expression, cortical areas in
mouse
Gene expression (Arc) Allen Brain Atlas
Paxinos Franklin areas SumsDB/WebCaret
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Summary

• NIF Level 3 registration works!
• Allows diverse queries across databases
  (federation)
• Currently still in pilot mode
• Many opportunities to extend, expand
• (remainder of Phase II and beyond)